Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Identification of Pseudomanas fluorescens Fic auto-AMPylation site

ABSTRACT: This project has the aim of characterizing the function of the Fic-1 protein of Pseudomonas fluorescens.

INSTRUMENT(S): TripleTOF 5600

ORGANISM(S): Pseudomonas Fluorescens Escherichia Coli

TISSUE(S): Prokaryotic Cell

SUBMITTER: Ernesto Nakayasu

LAB HEAD: Ernesto S. Nakayasu

PROVIDER: PXD003076 | Pride | 2016-02-01

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	100915_Canhua_Fic_1_A.wiff	Wiff
	100915_Canhua_Fic_1_A.wiff.scan	Wiff
	100915_Canhua_mFic_1_A.wiff	Wiff
	100915_Canhua_mFic_1_A.wiff.scan	Wiff
	msms.txt	Txt

Items per page:

1 - 5 of 5

Publications

Identification of Fic-1 as an enzyme that inhibits bacterial DNA replication by AMPylating GyrB, promoting filament formation.

Lu Canhua C Nakayasu Ernesto S ES Zhang Li-Qun LQ Luo Zhao-Qing ZQ

Science signaling 20160126 412

The morphology of bacterial cells is important for virulence, evasion of the host immune system, and coping with environmental stresses. The widely distributed Fic proteins (filamentation induced by cAMP) are annotated as proteins involved in cell division because of the presence of the HPFx[D/E]GN[G/K]R motif. We showed that the presence of Fic-1 from Pseudomonas fluorescens significantly reduced the yield of plasmid DNA when expressed in Escherichia coli or P. fluorescens. Fic-1 interacted wit ...[more]

PMID: 26814232

Similar Datasets

Identification of Fic substrates in bacteria

Project description:This project has the aim of characterizing the function of the Fic-1 protein of Pseudomonas fluorescens.

2016-02-01 | PXD003077 | Pride

Structural basis of chaperone regulation by a post-translational modification

Project description:The Hsp70 chaperone BiP is covalently modified with adenosine monophosphate (referred to as AMPylation) in order to adapt its activity to the fluctuating folding load within the endoplasmic reticulum. This modification is catalyzed by the only human representative of the family of filamentation induced by cyclic adenosine monophosphate (Fic) enzymes HYPE/FICD. The structural basis for BiP binding and AMPylation has remained elusive due to the low affinity of enzyme substrate complexes.

2021-04-27 | PXD022869 | Pride

AMpylation is a hallmark of human neuronal differentiation

Project description:The AMPylation is novel protein post-translation modification. In consist of attachment of the adenosine monophosphate onto the serine, threonine or tyrosine amino acid residues of the protein. This process is catalysed by bacterial effectors or in human by protein FICD (also called HYPE) which contain conserved fic domain. In our study we have focused on identification of the unknown AMPylated proteins and their function in human cells (HeLa, A549, SH-SY5Y, iPSCs, NPCs and neurons) and cerebral organoids (COs). For this purpose we designed and synthesized the small molecule N6-propargyl phosphoramidate adenosine (PAK-76) which was used for in situ labelling of the AMPylation in cells and COs. Subsequnetly the the propargyl tag was employed for preparation of chemical-proteomic samples which were measured by LC-MS/MS. This approach confirmed the known AMPylation of heat shock protein HSPA5 and found diverse group of novel AMPylation targets. Several cathepsins found as AMPylation targets were further characterized by identification of AMP binding site. Based on our chemical proteomic data we found out that neurons and neuronal like cells contain distinct AMPylatino pattern from other studied cell types. This also suggested the importance of the AMPylation in these cell types which were then studied in cerebral organoids by overexpressing the FICD wt and E234G highly active mutant. This led to the accelerated differentiation of progenitors into the neurons. Overall our approach is suitable for identification of the AMPylated proteins in living cells and led to characterization of FICD function.

2024-05-21 | PXD008394 | Pride

FICD activity and AMPylation remodelling modulate human neurogenesis

Project description:The AMPylation is novel protein post-translation modification. In consist of attachment of the adenosine monophosphate onto the serine, threonine or tyrosine amino acid residues of the protein. This process is catalysed by bacterial effectors or in human by protein FICD (also called HYPE) which contain conserved fic domain. In our study we have focused on identification of the unknown AMPylated proteins and their function in human cells (HeLa, A549, SH-SY5Y, iPSCs, NPCs and neurons) and cerebral organoids (COs). For this purpose we designed and synthesized the small molecule N6-propargyl phosphoramidate adenosine (pro-N6pA) which was used for in situ labelling of the AMPylation in cells and COs. Subsequnetly the the propargyl tag was employed for preparation of chemical-proteomic samples which were measured by LC-MS/MS. This approach confirmed the known AMPylation of heat shock protein HSPA5 and found diverse group of novel AMPylation targets. Several cathepsins found as AMPylation targets were further characterized by identification of AMP binding site. Based on our chemical proteomic data we found out that neurons and neuronal like cells contain distinct AMPylatino pattern from other studied cell types. This also suggested the importance of the AMPylation in these cell types which were then studied in cerebral organoids by overexpressing the FICD wt and E234G highly active mutant. This led to the accelerated differentiation of progenitors into the neurons. Overall our approach is suitable for identification of the AMPylated proteins in living cells and led to characterization of FICD function.

2019-12-04 | PXD015062 | Pride

The DNA-binding induced (de)AMPylation activity of a Coxiella burnetii Fic enzyme targets Histone H3

Project description:Intracellular bacterial pathogens such as Coxiella burnetii evade their host's immune response by secreting effector proteins that bind and modify host proteins, thereby reshaping cell signaling pathways that help establish a replication-friendly niche. Previous research has identified Filamentation induced by cyclic AMP (Fic) enzymes as effector proteins in bacterial infections that modify their target proteins via the post-translational modification AMPylation. Fic enzymes use adenosine triphosphate (ATP) as co-substrate to transfer the adenosine monophosphate (AMP) group to a hydroxyl-containing side chain of their target protein. Many representatives of this enzyme class contain an autoinhibitory helix that suppresses AMPylation activity in vitro by contacting the active site. The mechanisms reversing this inhibition are incompletely understood. Extensive studies of the only human Fic protein FICD have revealed that FICD can switch between AMPylation and the reversal of this modification, deAMPylation, by a monomer-dimer transition. However, so far FICD remained the only example where deAMPylation by dimerization could be shown. Here we identify the protein product of C. burnetii CBU_0822, termed C. burnetii Fic 2 (CbFic2), to AMPylate host cell histone H3 at S10 and S28. We show that CbFic2 is a bifunctional enzyme, both capable of AMPylation as well as deAMPylation, and is regulated by the binding of DNA via its C-terminal helix-turn-helix domain. We propose that CbFic2 is capable of AMPylation in its monomeric form, and that binding to DNA induces a deAMPylating dimer.

2024-01-26 | PXD040330 | Pride

Histone ADP Ribosylation - Serine is a new target residue for endogenous ADP-ribosylation on histones

Project description:ADPr sites on histones obtained from cells were directly identified. We have identified 12 unique ADPr sites in human osteosarcoma cells and report serine ADPr as a new type of histone mark that responds to DNA damage.

2016-12-22 | PXD005462 | Pride

Affinity purification of ADP-ribosylated proteins from A. thaliana plants expressing the Pseudomonas syringae type III effector AvrRpm1 (2.5 ug Af1521 Macro, technical replicate 1)

Project description:ADP-ribosylated proteins were enriched using the engineered Af1521 Macro domain (Nowak et al., https://doi.org/10.1038/s41467-020-18981-w) from transgenic A. thaliana plants expressing the Pseudomonas syringae type III effector AvrRpm1. Enriched proteins were analyzed by LC-MS/MS.

2023-09-28 | PXD045544 | Pride

Affinity purification of ADP-ribosylated proteins from A. thaliana plants expressing the Pseudomonas syringae type III effector AvrRpm1, DDA method (2.5 ug Af1521 Macro, technical replicate 1)

2023-09-28 | PXD045558 | Pride

Affinity purification of ADP-ribosylated proteins from A. thaliana plants expressing the Pseudomonas syringae type III effector AvrRpm1 (DDA method) followed by identification of phosphorylation on S/T

Project description:ADP-ribosylated proteins were enriched using the engineered Af1521 Macro domain (Nowak et al., https://doi.org/10.1038/s41467-020-18981-w) from transgenic A. thaliana lines expressing the Pseudomonas syringae type III effector AvrRpm1. Enriched proteins were analyzed by LC-MS/MS.

2023-09-28 | PXD045550 | Pride

Pseudomonas type III effector AvrRpm1 ADP-ribosylates Arabidopsis thaliana PHOSPHOLIPASE D GAMMA 3 (PLDGAMMA3)

Project description:Nicotiana benthamiana tissue expressing either PLDGAMMA3-3xHA-StrepII or co-expressing AvrRpm1-3xFlag and PLDGAMMA3-3xHA-StrepII were subjected to enrichment of ADP-ribosylated proteins using the engineered Af1521 Macro domain (Nowak et al., https://doi.org/10.1038/s41467-020-18981-w). A non-functional Af1521 G42E mutant of the engineered Macro domain was used as control. Enriched proteins were analyzed by LC-MS/MS.

2024-10-22 | PXD056607 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data